OpenMS  2.5.0
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ResidueDB Class Reference

residue data base which holds residues More...

#include <OpenMS/CHEMISTRY/ResidueDB.h>

Public Member Functions

Constructors and Destructors
virtual ~ResidueDB ()
 destructor More...
 
Accessors
Size getNumberOfResidues () const
 returns the number of residues stored More...
 
Size getNumberOfModifiedResidues () const
 returns the number of modified residues stored More...
 
const ResiduegetResidue (const String &name) const
 returns a pointer to the residue with name, 3 letter code or 1 letter code name More...
 
const ResiduegetResidue (const unsigned char &one_letter_code) const
 returns a pointer to the residue with 1 letter code name More...
 
const ResiduegetModifiedResidue (const String &name)
 Returns a pointer to a modified residue given a modification name. More...
 
const ResiduegetModifiedResidue (const Residue *residue, const String &name)
 Returns a pointer to a modified residue given a residue and a modification name. More...
 
const std::set< const Residue * > getResidues (const String &residue_set="All") const
 returns a set of all residues stored in this residue db More...
 
const std::set< StringgetResidueSets () const
 returns all residue sets that are registered which this instance More...
 
Predicates
bool hasResidue (const String &name) const
 returns true if the db contains a residue with the given name More...
 
bool hasResidue (const Residue *residue) const
 returns true if the db contains the residue of the given pointer More...
 

Protected Member Functions

Private Constructors
 ResidueDB ()
 default constructor More...
 
 ResidueDB (const ResidueDB &residue_db)
 copy constructor More...
 

Typedefs

typedef std::set< Residue * >::iterator ResidueIterator
 
typedef std::set< const Residue * >::const_iterator ResidueConstIterator
 
static ResidueDBgetInstance ()
 this member function serves as a replacement of the constructor More...
 

Iterators

ResidueIterator beginResidue ()
 
ResidueIterator endResidue ()
 
ResidueConstIterator beginResidue () const
 
ResidueConstIterator endResidue () const
 
void setResidues_ (const String &filename)
 sets the residues from given file More...
 

Assignment

boost::unordered_map< String, Residue * > residue_names_
 
Residueresidue_by_one_letter_code_ [256]
 
Map< String, Map< String, Residue * > > residue_mod_names_
 
std::set< Residue * > residues_
 
std::set< const Residue * > const_residues_
 
std::set< Residue * > modified_residues_
 
std::set< const Residue * > const_modified_residues_
 
Map< String, std::set< const Residue * > > residues_by_set_
 
std::set< Stringresidue_sets_
 
ResidueDBoperator= (const ResidueDB &aa)
 assignment operator More...
 
void readResiduesFromFile_ (const String &filename)
 reads residues from the given file More...
 
ResidueparseResidue_ (Map< String, String > &values)
 parses a residue, given the key/value pairs from i.e. an XML file More...
 
void clear_ ()
 deletes all sub-instances of the stored data like modifications and residues More...
 
void clearResidues_ ()
 clears the residues and all lookup structures More...
 
void clearResidueModifications_ ()
 clears the residue modifications and all lookup structures More...
 
void buildResidueNames_ ()
 builds an index of residue names for fast access, synonyms are also considered More...
 
void addResidue_ (Residue *residue)
 

Detailed Description

residue data base which holds residues

The residues stored in this DB are defined in a XML file under data/CHEMISTRY/residues.xml

By default no modified residues are stored in an instance. However, if one queries the instance with getModifiedResidue, a new modified residue is added.

Member Typedef Documentation

◆ ResidueConstIterator

typedef std::set<const Residue*>::const_iterator ResidueConstIterator

◆ ResidueIterator

typedef std::set<Residue*>::iterator ResidueIterator

Constructor & Destructor Documentation

◆ ~ResidueDB()

virtual ~ResidueDB ( )
virtual

destructor

◆ ResidueDB() [1/2]

ResidueDB ( )
protected

default constructor

◆ ResidueDB() [2/2]

ResidueDB ( const ResidueDB residue_db)
protected

copy constructor

Member Function Documentation

◆ addResidue_()

void addResidue_ ( Residue residue)
protected

◆ beginResidue() [1/2]

ResidueIterator beginResidue ( )
inline

◆ beginResidue() [2/2]

ResidueConstIterator beginResidue ( ) const
inline

◆ buildResidueNames_()

void buildResidueNames_ ( )
protected

builds an index of residue names for fast access, synonyms are also considered

◆ clear_()

void clear_ ( )
protected

deletes all sub-instances of the stored data like modifications and residues

◆ clearResidueModifications_()

void clearResidueModifications_ ( )
protected

clears the residue modifications and all lookup structures

◆ clearResidues_()

void clearResidues_ ( )
protected

clears the residues and all lookup structures

◆ endResidue() [1/2]

ResidueIterator endResidue ( )
inline

◆ endResidue() [2/2]

ResidueConstIterator endResidue ( ) const
inline

◆ getInstance()

static ResidueDB* getInstance ( )
static

this member function serves as a replacement of the constructor

◆ getModifiedResidue() [1/2]

const Residue* getModifiedResidue ( const Residue residue,
const String name 
)

Returns a pointer to a modified residue given a residue and a modification name.

The modified residue is added to the database if it doesn't exist yet.

Exceptions
Exception::IllegalArgumentif the residue was not found
Exception::InvalidValueif no matching modification was found (via ModificationsDB::getModification)

◆ getModifiedResidue() [2/2]

const Residue* getModifiedResidue ( const String name)

Returns a pointer to a modified residue given a modification name.

The "base" residue is looked up in ModificationsDB using the modification name. The modified residue is added to the database if it doesn't exist yet.

◆ getNumberOfModifiedResidues()

Size getNumberOfModifiedResidues ( ) const

returns the number of modified residues stored

◆ getNumberOfResidues()

Size getNumberOfResidues ( ) const

returns the number of residues stored

◆ getResidue() [1/2]

const Residue* getResidue ( const String name) const

returns a pointer to the residue with name, 3 letter code or 1 letter code name

◆ getResidue() [2/2]

const Residue* getResidue ( const unsigned char &  one_letter_code) const

returns a pointer to the residue with 1 letter code name

◆ getResidues()

const std::set<const Residue*> getResidues ( const String residue_set = "All") const

returns a set of all residues stored in this residue db

The possible residues are defined in share/OpenMS/CHEMISTRY/Residues.xml. At the moment the following sets are available: All - all residues stored in the file Natural20 - default 20 naturally occurring residues Natural19WithoutI - default natural amino acids, excluding isoleucine (isobaric to leucine) Natural19WithoutL - default natural amino acids, excluding leucine (isobaric to isoleucine) Natural19J - default natural amino acids, (isobaric leucine/isoleucine are marked by 'J') AmbiguousWithoutX - all amino acids, including ambiguous ones: B (asparagine or aspartate), Z (glutamine or glutamate), J (isoleucine or leucine) Ambiguous - all amino acids including all ambiguous ones (X can be every other amino acid) AllNatural - naturally occurring residues, including selenocysteine (U)

returns an empty set if the specified residue set is not defined

◆ getResidueSets()

const std::set<String> getResidueSets ( ) const

returns all residue sets that are registered which this instance

◆ hasResidue() [1/2]

bool hasResidue ( const Residue residue) const

returns true if the db contains the residue of the given pointer

◆ hasResidue() [2/2]

bool hasResidue ( const String name) const

returns true if the db contains a residue with the given name

◆ operator=()

ResidueDB& operator= ( const ResidueDB aa)
protected

assignment operator

◆ parseResidue_()

Residue* parseResidue_ ( Map< String, String > &  values)
protected

parses a residue, given the key/value pairs from i.e. an XML file

◆ readResiduesFromFile_()

void readResiduesFromFile_ ( const String filename)
protected

reads residues from the given file

Exceptions
Exception::ParseErrorif the file cannot be parsed

◆ setResidues_()

void setResidues_ ( const String filename)
protected

sets the residues from given file

Member Data Documentation

◆ const_modified_residues_

std::set<const Residue*> const_modified_residues_
protected

◆ const_residues_

std::set<const Residue*> const_residues_
protected

◆ modified_residues_

std::set<Residue*> modified_residues_
protected

◆ residue_by_one_letter_code_

Residue* residue_by_one_letter_code_[256]
protected

◆ residue_mod_names_

Map<String, Map<String, Residue*> > residue_mod_names_
protected

◆ residue_names_

boost::unordered_map<String, Residue*> residue_names_
protected

◆ residue_sets_

std::set<String> residue_sets_
protected

◆ residues_

std::set<Residue*> residues_
protected

◆ residues_by_set_

Map<String, std::set<const Residue*> > residues_by_set_
protected